Variant report

Variant	rs13302841
Chromosome Location	chr9:3459422-3459423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10115757	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs10115791	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs10117357	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs10117431	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs10117846	0.89[JPT][hapmap]
rs10124292	0.86[JPT][hapmap]
rs10124295	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10511447	0.86[JPT][hapmap]
rs10814096	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10814097	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10971599	0.88[JPT][hapmap]
rs10971667	0.88[JPT][hapmap]
rs10971806	0.84[CEU][hapmap]
rs10971976	0.87[ASN][1000 genomes]
rs10972042	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10972061	0.90[ASN][1000 genomes]
rs10972079	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10972081	0.81[EUR][1000 genomes]
rs10972156	0.87[ASN][1000 genomes]
rs12002215	0.88[JPT][hapmap]
rs12115798	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12337095	0.89[JPT][hapmap]
rs12339955	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs12340535	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs12341652	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12341737	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs12343385	0.84[CEU][hapmap]
rs12346432	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12347068	0.88[JPT][hapmap]
rs12347811	0.80[CEU][hapmap]
rs12347985	0.84[CEU][hapmap]
rs12554323	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13286511	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs13290412	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13295925	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs13297034	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs13298219	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13298908	0.84[CEU][hapmap]
rs13300358	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13300995	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13301035	0.82[ASN][1000 genomes]
rs13302664	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs16917371	0.88[JPT][hapmap]
rs16924266	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1998976	1.00[JPT][hapmap]
rs34086781	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34123151	0.87[EUR][1000 genomes]
rs34708788	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34770513	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35625648	0.87[EUR][1000 genomes]
rs35824006	0.80[EUR][1000 genomes]
rs36091570	0.85[ASN][1000 genomes]
rs3758195	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs3758196	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs4741825	0.84[CEU][hapmap]
rs4741829	0.83[CEU][hapmap]
rs57004251	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6476436	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs6476451	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7021584	0.86[JPT][hapmap]
rs7026530	0.88[JPT][hapmap]
rs7028812	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7029544	0.88[JPT][hapmap]
rs7040113	0.88[JPT][hapmap]
rs7041836	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs7043493	0.88[JPT][hapmap]
rs7045360	0.84[JPT][hapmap]
rs71506638	0.80[EUR][1000 genomes]
rs71506643	0.96[EUR][1000 genomes]
rs71506645	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs768485	0.86[JPT][hapmap]
rs7853728	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7854273	0.88[JPT][hapmap]
rs7864440	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs7864459	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9298952	0.88[JPT][hapmap]
rs9695619	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019324	chr9:3436845-3502815	ZNF genes & repeats Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3432400-3467800	Weak transcription	GM12878-XiMat	blood
2	chr9:3432600-3460600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:3435000-3473200	Weak transcription	Primary T cells from cord blood	blood
4	chr9:3438400-3472800	Weak transcription	Primary B cells from cord blood	blood
5	chr9:3447400-3478800	Weak transcription	Aorta	Aorta
6	chr9:3448000-3475800	Weak transcription	Fetal Intestine Small	intestine
7	chr9:3452200-3464200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:3455000-3483000	Weak transcription	Fetal Thymus	thymus
9	chr9:3456000-3460000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:3456200-3467600	Weak transcription	Ovary	ovary
11	chr9:3456200-3473200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:3458000-3467800	Weak transcription	A549	lung
13	chr9:3458400-3459600	Enhancers	Fetal Heart	heart
14	chr9:3458600-3459800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:3458800-3459600	Enhancers	Brain Germinal Matrix	brain
16	chr9:3458800-3460000	Enhancers	Fetal Brain Male	brain
17	chr9:3458800-3460200	Enhancers	Dnd41	blood
18	chr9:3459000-3459600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:3459000-3459600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:3459200-3460200	Weak transcription	Fetal Brain Female	brain
21	chr9:3459400-3461400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr9:3459400-3467600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:3459400-3467600	Weak transcription	Brain Anterior Caudate	brain
24	chr9:3459400-3467800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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